#!/bin/bash

## for nucleotide sequences;
perl phylo_tree.pl ../input/nt.phy -type nj  -outdir nj_nt/
perl phylo_tree.pl ../input/nt.phy -type ml -outdir ml_nt/
perl phylo_tree.pl ../input/nt.phy -type bayes  -outdir bayes_nt/

## for amino-acid sequences;
perl phylo_tree.pl ../input/aa.phy --type nj -d aa -t jtt -outdir nj_aa/
perl phylo_tree.pl ../input/aa.phy --type ml -d aa -m JTT -outdir ml_aa/
perl phylo_tree.pl ../input/aa.phy --type bayes -data protein  -rates invgamma -outdir bayes_aa/
